cool-seq-tool 0.15.0__tar.gz → 0.15.1__tar.gz

{cool_seq_tool-0.15.0 → cool_seq_tool-0.15.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cool_seq_tool
-Version: 0.15.0
+Version: 0.15.1
 Summary: Common Operation on Lots of Sequences Tool
 Author: Kori Kuzma, James Stevenson, Katie Stahl, Alex Wagner
 License: MIT License
@@ -46,7 +46,7 @@ Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: asyncpg
 Requires-Dist: boto3
-Requires-Dist: agct>=0.1.0-dev1
+Requires-Dist: agct>=0.2.0rc1
 Requires-Dist: polars~=1.0
 Requires-Dist: biocommons.seqrepo
 Requires-Dist: pydantic<3.0,>=2.0

{cool_seq_tool-0.15.0 → cool_seq_tool-0.15.1}/pyproject.toml

@@ -26,7 +26,7 @@ license = {file = "LICENSE"}
 dependencies = [
     "asyncpg",
     "boto3",
-    "agct >= 0.1.0-dev1",
+    "agct >= 0.2.0rc1",
     "polars ~= 1.0",
     "biocommons.seqrepo",
     "pydantic >=2.0,<3.0",

{cool_seq_tool-0.15.0 → cool_seq_tool-0.15.1}/src/cool_seq_tool/mappers/liftover.py

@@ -6,7 +6,8 @@ Currently only supports GRCh37 <-> GRCh38
 import logging
 from os import environ
 
-from agct import Converter, Genome
+from agct import Assembly as AgctAssembly
+from agct import Converter
 
 from cool_seq_tool.schemas import Assembly
 from cool_seq_tool.utils import process_chromosome_input
@@ -43,13 +44,13 @@ class LiftOver:
         """
         self.from_37_to_38 = Converter(
             chainfile=chain_file_37_to_38 or LIFTOVER_CHAIN_37_TO_38,
-            from_db=Genome.HG19,
-            to_db=Genome.HG38,
+            from_assembly=AgctAssembly.HG19,
+            to_assembly=AgctAssembly.HG38,
         )
         self.from_38_to_37 = Converter(
             chainfile=chain_file_38_to_37 or LIFTOVER_CHAIN_38_TO_37,
-            from_db=Genome.HG38,
-            to_db=Genome.HG19,
+            from_assembly=AgctAssembly.HG38,
+            to_assembly=AgctAssembly.HG19,
         )
 
     def get_liftover(
@@ -77,9 +78,9 @@ class LiftOver:
         """
         chromosome = process_chromosome_input(chromosome, "LiftOver.get_liftover()")
         if liftover_to_assembly == Assembly.GRCH38:
-            liftover = self.from_37_to_38.convert_coordinate(chromosome, pos)
+            liftover = self.from_37_to_38.convert_coordinate(chromosome, pos, pos)
         elif liftover_to_assembly == Assembly.GRCH37:
-            liftover = self.from_38_to_37.convert_coordinate(chromosome, pos)
+            liftover = self.from_38_to_37.convert_coordinate(chromosome, pos, pos)
         else:
             _logger.warning("%s assembly not supported", liftover_to_assembly)
             liftover = None

{cool_seq_tool-0.15.0 → cool_seq_tool-0.15.1}/src/cool_seq_tool/resources/status.py

@@ -114,9 +114,9 @@ async def check_status(
             chain_file_38_to_37=chain_file_38_to_37,
         )
     except (FileNotFoundError, ChainfileError):
-        _logger.exception("agct converter setup failed")
+        _logger.exception("`agct` converter setup failed")
     except Exception as e:
-        _logger.critical("Encountered unexpected error setting up agct: %s", e)
+        _logger.critical("Encountered unexpected error setting up `agct`: %s", e)
     else:
         status["liftover"] = True
 

{cool_seq_tool-0.15.0 → cool_seq_tool-0.15.1}/src/cool_seq_tool.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cool_seq_tool
-Version: 0.15.0
+Version: 0.15.1
 Summary: Common Operation on Lots of Sequences Tool
 Author: Kori Kuzma, James Stevenson, Katie Stahl, Alex Wagner
 License: MIT License
@@ -46,7 +46,7 @@ Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: asyncpg
 Requires-Dist: boto3
-Requires-Dist: agct>=0.1.0-dev1
+Requires-Dist: agct>=0.2.0rc1
 Requires-Dist: polars~=1.0
 Requires-Dist: biocommons.seqrepo
 Requires-Dist: pydantic<3.0,>=2.0

{cool_seq_tool-0.15.0 → cool_seq_tool-0.15.1}/src/cool_seq_tool.egg-info/requires.txt

@@ -1,6 +1,6 @@
 asyncpg
 boto3
-agct>=0.1.0-dev1
+agct>=0.2.0rc1
 polars~=1.0
 biocommons.seqrepo
 pydantic<3.0,>=2.0